it = parameters.find("list");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["list"] = inputDir + it->second; }
}
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir = "";
- outputDir += hasPath(listFile); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(listFile); //if user entered a file with a path then preserve it
}
//check for optional parameter and set defaults
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { m->mothurOut("label is a required parameter for the otu.hierarchy command."); m->mothurOutEndLine(); abort = true; }
else {
- splitAtDash(label, labels);
+ m->splitAtDash(label, labels);
if (labels.size() != 2) { m->mothurOut("You must provide 2 labels."); m->mothurOutEndLine(); abort = true; }
}
}
ofstream out;
- string outputFileName = outputDir + getRootName(getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
- openOutputFile(outputFileName, out);
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
+ m->openOutputFile(outputFileName, out);
//go through each bin in "big" otu and output the bins in "little" otu which created it
for (int i = 0; i < lists[1].getNumBins(); i++) {
//open file
ifstream in;
- openInputFile(listFile, in);
+ m->openInputFile(listFile, in);
//get first list vector in file
ListVector* list = NULL;
pos = in.tellg();
lastPos = pos;
list = new ListVector(in);
- gobble(in);
+ m->gobble(in);
lastLabel = list->getLabel();
}
}
//you have a label the user want that is smaller than this label and the last label has not already been processed
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = list->getLabel();
int savePos = in.tellg();
if (!in.eof()) {
pos = in.tellg();
list = new ListVector(in);
- gobble(in);
+ m->gobble(in);
}else { list = NULL; }
}